In this project, we propose to study kidney transplant patients with three possible outcomes (acute rejection, chronic allograft nephropathy, and long-term normal functioning transplants). Our objective is to identify the genetic factors associated with these clinically distinct outcomes. Our first thesis is that understanding the genetic and molecular factors associated with the success or failure in renal transplantation will lead to personalized immunosuppressive therapy that increases the success rate of transplantation while decreasing drug-related morbidity and mortality. Our second thesis is that by understanding the genetic elements of donor organ responses to transplantation that determine clinical outcomes, we can identify, a whole new approach to discovering new pathways and drug targets to enhance transplantation success and safety. For each of the three clinically distinct transplant phenotypes, we will identify genetic variations in the 500 gene candidates identified in Projects 1 and 2 and look for genetic association of single nucleotide polymorphism (SNP) markers in these genes. A unique feature of our proposal is that differentially expressed genes in the donor organ will also be pursued with donor DNA. In collaboration with Affymetrix, we will take advantage of two powerful genetic tools to increase the speed of discovery while keeping the cost low. We will also leverage the knowledge gained from the International Haplotype Map Project and take advantage of a pooling strategy for SNP genotyping. The specific aims of this project are: 1. Screen gene candidates implicated by their differential gene or proteome expression profiles between cases and controls for genetic association by comprehensive DNA resequencing with high-density oligonucleotide microarrays. 2. Screen gene candidates using "haplotype-tag SNPs" (htSNPs) from the HapMap Project for genetic association using a pooled SNP genotyping approach followed by individual SNP genotyping of associated SNPs. 3. Conduct whole-genome screening using a set of high-density SNP microarrays for genetic association. 4. Validate the genetic association by testing a second cohort of donors and recipients obtained prospectively and archived during the first four years of the program project.